EpiTrans: Estimation of epidemic transmissibility in time and space

2021.11.04 Example

devtools::install_github("wenlab501/EpiTrans")

library(EpiTrans)
EpiTransLibrary()

Dengue

Calculate

x=dengue$long
y=dengue$lat
t=dengue$date
dengue.R=Rj(x,y,t)
Rd=dengue.R$Rj

Plot points

plot_points(x,y)

## tmap mode set to interactive viewing

plot_points(x,y,basemap = Taiwan)

## tmap mode set to interactive viewing

plot_points(x,y,basemap = Taiwan,interact = F)

## tmap mode set to plotting

plot_points(x,y,Rj=Rd)

## tmap mode set to interactive viewing

plot_points(x,y,Rj=Rd,basemap = Taiwan,interact = F)

## tmap mode set to plotting

plot_points(x,y,t=t,basemap = Taiwan)

## tmap mode set to interactive viewing

Plot grids

plot_grid(x,y)

## tmap mode set to interactive viewing

plot_grid(x,y,Rj=Rd)

## tmap mode set to interactive viewing

plot_grid(x,y,Rj=Rd,basemap = Taiwan)

## tmap mode set to interactive viewing

plot_grid(x,y,Rj=Rd,basemap = Taiwan,interact = F)

## tmap mode set to plotting

Plot hexagons

plot_hex(x,y,Rj=Rd,basemap = Taiwan)

## tmap mode set to interactive viewing

plot_hex(x,y,Rj=Rd,basemap = Taiwan,interact = F)

## tmap mode set to plotting

Plot KDE

plot_kde(x,y,basemap = Taiwan)

## tmap mode set to interactive viewing

## Using centroids instead of provided `grid` geometries to calculate KDE estimates.

plot_kde(x,y,basemap = Taiwan,interact = F)

## tmap mode set to plotting
## Using centroids instead of provided `grid` geometries to calculate KDE estimates.

Plot transmission likelihood

plot_trans(dengue.R)

## Loading required package: raster

## Warning: package 'raster' was built under R version 4.0.5

## Loading required package: sp

## Warning: package 'sp' was built under R version 4.0.5

## 
## Attaching package: 'raster'

## The following object is masked from 'package:MASS':
## 
##     select

## The following object is masked from 'package:dplyr':
## 
##     select

COVID-19

Calculate

covid = GeoLocater(covid19,RndPts)
region = covid$region
date = covid$date
X = covid$x
Y = covid$y
covid.R=Rj(X, Y, date, GI.pdf = lpdf_GI(5.2,1.5), unit_coord = "meter")
Rc = covid.R$Rj
Rc[Rc==Inf]=max(Rc[Rc!=Inf])

Plot points

plot_points(X,Y,crs=3826)

## tmap mode set to interactive viewing

plot_points(X,Y,crs=3826,basemap = Taipei)

## tmap mode set to interactive viewing

plot_points(X,Y,crs=3826,basemap = Taipei,interact = F)

## tmap mode set to plotting

plot_points(X,Y,crs=3826,Rj=Rc)

## tmap mode set to interactive viewing

plot_points(X,Y,crs=3826,Rj=Rc,basemap = Taipei,interact = F)

## tmap mode set to plotting

plot_points(X,Y,crs=3826,t=date,basemap = Taipei)

## tmap mode set to interactive viewing

Plot grids

plot_grid(X,Y,crs=3826)

## tmap mode set to interactive viewing

plot_grid(X,Y,crs=3826,Rj=Rc)

## tmap mode set to interactive viewing

plot_grid(X,Y,crs=3826,Rj=Rc,basemap = Taipei)

## tmap mode set to interactive viewing

plot_grid(X,Y,crs=3826,Rj=Rc,basemap = Taipei,interact = F)

## tmap mode set to plotting

Plot hexagons

plot_hex(X,Y,crs=3826,Rj=Rc,basemap = Taipei)

## tmap mode set to interactive viewing

plot_hex(X,Y,crs=3826,Rj=Rc,basemap = Taipei,interact = F)

## tmap mode set to plotting

Plot KDE

plot_kde(X,Y,crs=3826,basemap = Taipei)

## tmap mode set to interactive viewing

## Using centroids instead of provided `grid` geometries to calculate KDE estimates.

plot_kde(X,Y,crs=3826,basemap = Taipei,interact = F)

## tmap mode set to plotting
## Using centroids instead of provided `grid` geometries to calculate KDE estimates.

Plot polygons

plot_polygons(region,Taipei)

## tmap mode set to interactive viewing

plot_polygons(region,Taipei,interact = F)

## tmap mode set to plotting

Animate polygons

animate_polygons(region,date,Taipei)

animate_polygons(region,date,Taipei,"week")

#### Plot transmission likelihood

plot_trans(dengue.R)

plot_trans(covid.R)